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NERSC response: There are not many alternatives to gdb on linux. STAR is looking into purchasing Totalview (which has a GUI interface and works well with both gcc and pgf). The licenses are expensive ($5700/00 for 8 floating licenses +20%/year maintenance fee - that is a cost of 1TB of disk vault), but we will consult with all the group representatives to find out whether they are interested in financing it.
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Our application seems to perform particularly badly on SP machines, where we typically get around 6% peak floating point performance. We've worked at applying various compiler optimizations but have not succeeded in improving the performance beyond this limit. This is in contrast to other platforms (ia32, compaq, hitachi) where we typically run at 15-25%.
I find the emails useful, however I would like to receive multiple reminders on the same issue. I accept that maybe other people don't want as much traffic, but if a major change is about to happen in a months, then from about 10 days in advance I would like to get an email about this every day. Maybe it is possible to configure this on a per user or per mailing list basis so that users can define how often they want to get this kind of information.
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Introducing one more queue would have a real effect only if we allocated a group on nodes that would run that semi-medium or short queue exclusively. That would only further increase resource fragmentation and encourage users to game the system by subdividing jobs which only increases the LSF overhead and wastes resources. We closely monitor the cluster load and job length and if a need shows up we will adjust queue length and node assignments, but we do not plan on adding more queues.
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NERSC compares very well with other centers. As I said, the major problem with NERSC is system crowding; this is likely the result of the high demand caused by the quality services you provide.
I have only used LLNL and NERSC. Both do a great job and share many personality traits.
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NERSC response:The two largest PDSF users groups require the pgf compiler, so we can look at the INTEL FORTRAN license as an addition and not a replacement. Additionally INTEL FORTRAN does not work with the Totalview debugger, currently the only decent option for debugging jobs that are a mixture of FORTRAN and C++ on linux. Also INTEL licenses are pricey, but we will check what kind of user base is there for this compiler and see whether this is something we can afford.
Also it helps to look at this issue in a different way. In times of high demand everybody is getting what they paid for (their share) and when STAR is not running, other groups can use the resource "for free".
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PHASE 4 CLINICAL TRIALSA Phase IV Clinical trial is a
NERSC response: The hardware failure rate for hard drives is comparable to the average failure rate for commodity hard-drives. It may appear artificially high as we have a large number (>>600) of them. However, in order to minimize impact of those failures on our users we closely monitor the market and adopt solutions that ease that allow for transparent drive replacements. Right now (mid-October 2002) we are finishing a conversion of the disk vaults from a software to a hardware raid (~33 done and ~5 more to go). That not only improves their performance, but also makes them more reliable and easier to replace hard drives without affecting the users.
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NERSC response: There is a section in a tutorial for new users that explains how system calculates priorities. That section will be linked from the batch page as the issue of priorities is of great interest to many users.
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NERSC response: Disk vaults are assigned to experiments based on their financial contribution. STAR subdivided their disk space between the physics working groups and Doug Olson ([email protected]) should be contacted for more details. A list of disk vaults with their current assignments is available at: PDSF staff (by request from the experiments) does not interfere with how the disk space is subdivided between the users but if experiments wish we can run a cleanup script (details set by the requester). Currently this is in place on pdsfdv15.
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The other center I used extensively is the NCSA at UI, Urbana-Champaign. I started using NERSC again after a gap of few years (mainly as a result of NCSA doing all the things I need much better than NERSC) and have to say that it has vastly improved. It now compares quite favorably with NCSA. My only problem (complaint) now is the lack of plotting software at NERSC ( at NCSA I can use on the origin machines AVS, Techplot etc ,). The available software such as DX seem to be poorly configured (DX for instance doesn't support netcdf as it is presently configured on Seaborg).
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Account support has also been very good. I also appreciate the seeming concern about security.
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Excellent support services from everyone. I'm especially happy to have Iwona as a resource at NERSC. She knows her stuff, is always helpful and tries to respond quickly.
PHASE 1 CLINICAL TRIALSPhase 1 Clinical Trials are th
Big fast machines with large memory and excellent fortran environment. NERSC should continue to increase the speed and memory of its machines as the technology evolves.
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For various reasons, I never go to actual classes at LBNL for all the training stuff. One reason is that one wants to avoid repeat material. Having the class stuff on the web as html (not just powerpoint which linux machines can't read) is great and more useful in the long run.
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NERSC provides access to very high performance computing facilities on a platform with a simple interface, making development easy. Information services, training, account management, and consulting are all excellent.
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I was not aware of all these useful sources of information. Will use them more in the future.
The present default version of Totalview on the IBM SP does not work correctly with our code, making debugging very difficult. We had been using the previous version, which did work but is no longer available. We would be very grateful if it were returned to service.
TOPICS TO BE DISCUSSEDClinical Trials – Definitions, Importance of trials Role of Clinical trials in Clinical
I began to use the computer less than a year. But I still have many problems to run my programs. Most my programs are running at Lawrence Livermore National Laboratory but I am having problem even to make an executable file.
Of all the ones I used, it is the best. The old Pittsburgh supercomputer center had equally good (if not better) consulting/help, but no good web pages and the computers weren't as good. The other center I use a lot was the SDSC bluehorizon.
Losing Cray's totalview and debuggers is a real loss as they were very superior to what's available on the Cray's. I also don't like XProfiler too much.
The storage system does not always respond. This is fatal when the data for batch jobs is too large to fit on the local disk. I had several of my batch jobs hang while trying to copy the data from the HPSS system to temporary disk space.
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At LRZ Muenchen the maximum runtime is 32 hours for a job and the system places no other restrictions on number of cpu, memory. I use that regularly for production runs and it is great. At lemieux at PSC there is an option to specify qsub -I on which one gets a collection of nodes for interactive use. This allows for very rapid debugging, since one bypasses the queue.
The justification is that no analysis could be completed without embedding and many users run on pico-DST's produced by Masashi. STAR users should direct their comments regarding share settings within STAR to its computing leader (Jerome Laurent - [email protected]). NERSC staff does not set policies on the subdivision of shares within the STAR group.
It is expensive to come as a university researcher and allocate time. I think NERSC needs more partnerships on the best science areas.
The debugging tool was a bit tricky to use, and I should probably come to one of the classes/training sessions. This would allow me to really use the debugger as a tool.
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Allocation of processors in chunks smaller than 16 would be useful. More and longer regular_long time should be allocated.
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Single-processor speeds on this machine have fallen behind the curve; we have ceased development on this platform. Communication speeds are excellent, however.
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Other computing services I have used have been operated by non-professional staff or pretty small in size. The NERSC does an outstanding job of maintaining the system.
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There is a terrible interface with desktop computers. I cannot access my PDSF files with a GUI interface. There ways to do it such as NFS or SAMBA, but NERSC does not implement them because of security reasons. There needs to be a way for me to access my NERSC files as if they are on my laptop. AFS works well, but NERSC only supports that access for a small amount of disk space. Modern computing uses a GUI interface. NERSC needs to support that interface.
There is an abundance of documentation I have benefited from. Account support has also been very good. I also appreciate the seeming concern about security.
NERSC should go almost exclusively to web tutorials and web based training. Courses on site are just out of the question to go, since it is much too expensive to fly to the west coast.
We use the queue length to manage the frequency with which job slots open. The short queue runs exclusively on 30 CPU's (as well as on all the other CPU's sharing with medium and low). This means that on average a slot for a short job opens every 2 minutes. These settings provide for a reasonable debugging frequency at the expense of those 30 nodes being idle when there are no short jobs.
Getting better and better with time. Resolution of obscure or hard to detect problems is now outstanding. We had a strange segfault problem that was solved by going to 64bit address mode, I'd never have guessed that.
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Many thanks for the recent updates. Some more please as time allows.
Hi Dennis, Thanks for the additions. I think you've mixed up 2 additions from October 7: you added G-ARNL as a Forney, whereas it's a PA-22-108, and G-ARHF (which is a Forney) you missed completely!
I wish it was easier to get a node when running interactively. I realize that most of the nodes are running batch jobs, but it might make sense to allocate more nodes for interactive use.
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NERSC response: Indeed disk vaults have poor performance while serving multiple clients. Very recently we converted them from software to hardware raid which improved their bandwidth. We also brought in an alternative solution for testing, the so called "beta" system. PDSF users loved the performance (instead of couple tens, it could serve couple hundred clients without loss in performance), but such systems are much more expensive (currently factor of 4 at least) and at the end the experiments decided to go with a cheaper hardware raid solution. We are watching the market all the time and bring in for testing various solutions (like "beta" and "Blue Arc") and if anything that the experiments can afford comes by, we will purchase it.
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Thanks for adding the last list so quickly. There does appear to be an error though.
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I have a code (check my blog) which uses a lot of FFTs and thus has a decent amount of global communication. The only problem that I have with the IBM SP is that communication between the nodes is too slow. Thus, it takes the same amount of time to run my code on the Cray T3E as it does to run on the IBM SP.
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It would help me enormously if you had emacs or some other text editor other than VI on the log in node. I hate VI and have to do editing locally and do more file transfers than I would like. When debugging, it is useful to make quick changes on the local computer.
NERSC response:PDSF is a form of cooperative. NERSC helps to finance it (~15%) All the groups get access that is proportional to their financial contribution. These "Shares" can be checked by issuing a bhpart command on any of the interactive nodes. STAR is the most significant contributor, thus it gets a high share. However, the system is not quite full all the time - please check our record for the past year at:.
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The SP seems a good solid machine on which to do reliable runs over many processors. We've had much worse experience with large PC clusters, and it's been great to run on seaborg.
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I think NERSC should do more system changes on weekends. This would affect the users less.
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NERSC response: High Bandwidth nodes (compute nodes with a large local disks - 280GB in addition to 10GB /scratch) are all in the medium queue and access is governed by the same set of rules as for any other compute node in the medium queue. The only restriction is the allocation of the 280GB disk where only the starofl account has write privileges. That is necessitated by the type of analysis STAR does and the experiment financed purchase of this disk space. If you are from STAR and do not agree with this policy, please contact Doug Olson ([email protected]).
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I also use SDSC and many local (university) centers. NERSC has a huge lead on all of them.
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Large jobs will sit in queue too long and are effectively impossible to run. Thus from a user perspective NERSC is not a large machine.
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NERSC response: Security threats indeed disrupted development of software that was unifying the desktop and the compute environments. There is a new generation growing though based on the Globus toolkit. We are monitoring this development but it is not ready for the production yet.
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Possibly more could be done to help remote users make the best use of NERSC. Possibly many users would benefit from periodic visits, as opposed to classes.
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Improved debug and interactive turnaround during prime time by setting aside 5% of the SP compute pool for interactive and debug jobs from 5:00 AM to 6:00 PM Pacific Time Monday to Friday. This year's rating for SP: ability to run interactively went up by 0/8 points.
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Among the supercomputing facilities I tried until now, NERSC excels in most aspects. I am most satisfied with the overall stability of the system. This must come from the outstanding competence of the technicians.
We went over our allotted HPSS allocation, but thank you for being flexible about this. We plan to use this storage for all our simulations for years to come.
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These other centers have failed to understand that there are specific areas of excellent science where linear scaling with huge # of CPUs is merely impossible, because of the nature of the problem dealt with, not because of code deficiencies. I strongly encourage NERSC to stay away from that logic. Excellent Science needs both super-large but also medium range parallel computing.
However, for remote visualization it would be more useful to use gridftp to access the data on seaborg directly from my desktop. We didn't have the technology to do this during our last simulations but I would like to try it for the next one.
I've been incredibly happy with the SP. Batch queue turnaround times are very quick, and one can usually get away with the low queue on weekends. We've investigated efficiency quite extensively and found that we can run on 2-4 nodes fairly effectively and have run on up to 16 nodes (16 processors per node, in all cases).
The new authentication system for hpss seems to be incompatible with some windows OS secure shell soft. Since the change was mande I have not been able to connect using my laptop. I am still trying to get this fixed with the help of the support people here at LLNL, but no good news so far.
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This is one of the best features of the web site, and is a easy and quick tool for both daily monitoring and the entire allocation process. I especially like how easy the ERCAP is to roll over previous allocation requests and save them while you continue working on them.
NERSC is the top high performance computing center in my opinion. I also compute at NCAR, ORNL, PSC, and LANL. No other center provides the response or support that NERSC does.
Consider dedicating a few nodes to interactive shared use for debugging purposes. SDSC does this; performance on the shared nodes is assuredly terrible, but you can at least fire up totalview on a parallel job without loadleveler rejecting it due to lack of free nodes. This situation has become the bane of my existence at NERSC in recent months.
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We've gotten some custom mods to the system for our use which has been very helpful. Consultants are always available and helpful.
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NERSC response:PDSF is a networked distributed computing environment used to meet the detector simulation and data analysis requirements of large scale High Energy Physics (HEP) and Nuclear Science (NS) investigations. For updated information about the facility, check out the PDSF Home Page.
Are you on Kurzarbeit or how come, that you invest seemingly even more time adding our requests,lately? If so, I hope it's to your convenience.
I wish I would come to some of the training classes, but it always seems as if I've already got too many things going on. I'm sure I could be using the NERSC facilities more effectively with a little guidance. But the web site has been great at making the training an after thought rather than a necessary step.
The major way in which NERSC could improve would be to upgrade its computing facilities more aggressively. It is surprising to me that NERSC trails the NSF centers in total computing power.